bacteria

Gut Instinct: How Diets Shape the Unique Composition of Indian Guts

Researchers from IISER Bhopal decided to carry out an in-depth study of the diversity of Indian gut flora by comparing and contrasting the microbiome of populations from two parts of the country with very disparate diets.

In a recent study, researchers show that Indian guts harbour a unique microbial population compared to other countries, and that the diverse diets within the country are associated with different gut microbes.

“Diet has been known to be the key driver in shaping the gut microbiome. Indian population has diverse lifestyles and food habits and so far, the Indian gut genome is not well explored,” states Vineet Sharma, a scientist at Indian Institute of Science, Education and Research (IISER) Bhopal and a member of the research team who performed the study. India also has the highest prevalence of diabetes in the world, with 53% of deaths in India attributed to diabetes and cardiovascular diseases. India thus presents an interesting case study to understand the interplay between gut, diet and health.

In this first-ever large-scale study, Sharma and colleagues analysed the microorganisms in gut of 110 healthy individuals to uncover the microbial diversity in India. The researchers sampled individuals from two locations with distinct diets: Bhopal in the North-Central region and Kerala from the southern part of India. The Bhopal population predominantly consumes a carbohydrate-rich diet, including plant-derived products, wheat and trans-fat food (high-fat dairy, sweets and fried snacks), whereas, the Kerala population commonly consumes an omnivorous diet comprising rice, meat, and fish.

Researchers collected faecal samples from the volunteers, froze it within 30 min of collecting, and used it to sequence the microbiome (the combined genetic material of all the microorganisms present in a sample). A common method used for such purpose is the sequencing of the 16S rRNA gene. This gene consists of a region that is variable in different microorganisms, allowing the classification of different microbes. Using this analysis, the researchers found a total of 943,395 genes that were unique to the Indian microbiome.

Also read: Depressed People Have Low Levels of Two Bacteria in Their Guts: Study

The microbiome of the Indian population was also compared to the microbiome of other countries, such as USA, China, and Denmark. “One of the most interesting results was the much higher levels of Prevotella species in Indian gut microbiome compared to the other populations,” says Sharma. Prevotella has been previously observed in communities that consume a plant-rich diet and is associated with vegetarianism.

The differences in the microbial population within the country were also studied. The microbiome of participants from Bhopal was enriched in species from genus Prevotella, while the same from Kerala was enriched in species of Bifidobacterium, Ruminococcus, Clostridium and Faecalibacterium.

The authors propose these differences could arise due to the differences in the diet of the two locations. Using a method that annotates functions to genes, they showed that the Bhopal microbiome was enriched in genes involved in breaking down plant polysaccharides, while Kerala microbiome had genes involved in degrading lipids and proteins, indicating its animal-based diet.

Metabolites are small molecules produced during metabolism and can reveal insights on lifestyle and metabolic changes. An analysis of metabolites in the faeces showed a high concentration of saturated fatty acids and branched chain fatty acids in Bhopal microbiome, while the Kerala microbiome had short chain and medium chain fatty acids, presumably due to the high consumption of coconut oil in Kerala.

“Both branched-chain fatty acids (BCFA) and short-chain fatty acids (SCFAs) play an important role in the maintenance of health and elevated concentration of BCFAs may trigger the progression of different diseases,” says Bhabhatosh Das, a scientist at the Translational Health Science And Technology Institute (THSTI) who was not associated with the study.

It is known that the north-Indian population is predisposed towards diabetes and cardiovascular diseases. Further studies like these on diabetic and obese individuals can provide more insights into such predispositions towards diseases.

This article has been republished from IndiaBioscience. Read the original article.

Is There More to Gene Editing Than Creating ‘Designer’ Humans?

It may have greater consequences than climate change or unleashing the energy of the atom.

Today, the scientific community is aghast at the prospect of gene editing to create ‘‘designer” humans. Gene editing may be of greater consequence than climate change, or even the consequences of unleashing the energy of the atom.

CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. This is the immune system that bacteria developed to protect themselves from infections by bacteriophages — the most abundant life form on the planet.

Smaller than any known life form

Bacteriophages were discovered in Paris by Felix d’Hérelle at the Pasteur Institute in 1917. He was studying a subset of patients spontaneously recovering from dysentery. D’Hérelle proposed that an antimicrobe smaller than any known life form had killed the bacteria in infected patients. He demonstrated conclusively the existence of this new life form, and named them bacteriophages: viruses that attack bacteria.

Also Read: Study Finds Antibiotic Resistance Gene in Fresh Food Samples

The bacteriophage has been studied intensely: its beauty was revealed with the electron microscope and its genome was the first life form sequenced.

Responding to a bacteriophage attack

In 2007, Rodolphe Barrangou and Philippe Horvath of the food production company Danisco collaborated with Sylvain Moineau of Laval University to solve a long-standing problem in yogurt production. They asked: Why were bacteria that were essential for the production of yogurt and cheese susceptible to bacteriophage attack, and how could this be prevented?

Barrangou, Horvath and Moineau made the astonishing discovery that bacteria actually had an immune system.

CRISPR: Acquired Bacterial Immune Systems.

After an initial bacteriophage attack, a small number of surviving bacteria would recognize the DNA of the newly attacking bacteriophages. The surviving bacteria would then mount an immune response leading to the death of the bacteriophages. The bacteria that survived a phage attack would embed a fragment of bacteriophage DNA within their bacterial genome to serve as a “memory” of the infection.

Also Read: Explained: US Court Settles Bitter Gene Editing Patent Case, Confusion Lingers

Target and sever

Barrangou, Horvath and Moineau then discovered how the invading bacteriophages were eliminated. Upon recognition of the newly invading bacteriophage, the bacteria would target and sever the DNA of the invading bacteriophage.

Fond de recherche de Québec: CRISPR-Cas9 : L’origine de la découverte | Sylvain Moineau.

Biologists Jennifer Doudna and Emmanuelle Charpentier discovered further that “guides” had evolved in the bacterial immune system. Any bacteriophage whose DNA corresponded to the acquired memory fragment from a prior infection would be recognized and severed by a “guided” elimination machinery. Together, the bacterial immune system encompassing memory fragments of the bacteriophage DNA and the bacterial response machinery are known as the CRISPR-Cas9 system.

Commercial exploitation of the discovery followed. Doudna, Charpentier and others recognized that this new biological system could be exploited to edit genes in any life form.

Bozeman Science: What is CRISPR?

The CRISPR-Cas9 system is not the first gene-editing system to be discovered. The late biochemist Michael Smith, while at the University of British Columbia, was awarded a Nobel Prize in 1993 for the discovery of a chemical means of gene editing with applications relevant to cancer and other diseases.

UBC Science: The Legacy of Dr. Michael Smith.

Bacteriophages as a potential solution

D’Hérelle observed that the same bacteriophage isolated from patients recovering from dysentery could be used to protect rabbits from an otherwise fatal infection. Coming before the discovery of antibiotics, d’Hérelle’s discovery inspired Sinclair Lewis to feature bacteriophage therapy of humans in his Pulitzer Prize-winning novel Arrowsmith.

One of the largest collections of bacteriophages globally is at Laval University. Sylvain Moineau is the curator, and the collection is named after Felix d’Hérelle.

Also Read: The DNA Detectives Hunting the Causes of Cancer

The hope now is that bacteriophage therapy may be considered a potential solution to antibiotic resistance. However, any expectations of phage therapy are dwarfed by the current exploitation of the commercial benefits of the CRISPR-Cas9 system.

Today, the consequences of opening a Pandora’s Box are upon us. The application of the CRISPR-Cas9 system to generate designer humans through “germ-line” gene editing of harvested human eggs would create permanent changes that continue through successive generations, and the fears over these actions may be comparable to the consequences of nuclear warfare and climate change.

But there are other potential applications of “non-germline” CRISPR-Cas9, like the gene editing of disease. This has recently been successfully accomplished for muscular dystrophy in dogs. Akin to the myth of Pandora’s Box, the pessimism about “germ-line” gene editing may be offset by the hope for future benefit to humankind.

John Bergeron gratefully acknowledges Kathleen Dickson as co-author.

John Bergeron is an Emeritus Robert Reford Professor and Professor of Medicine at McGill, McGill University.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

I, Holobiont. Are You and Your Microbes a Community or a Single Entity?

Scientists have discovered more and more plants and animals that are accompanied by a jostling menagerie of internal and external fellow-travellers and a species called holobiont, a unique combination of a host, plus all of the resident microbes that live in it and on it.

Cicadas might be a pest, but they’re special in a few respects. For one, these droning insects have a habit of emerging after a prime number of years (7, 13, or 17). They also feed exclusively on plant sap, which is strikingly low in nutrients. To make up for this deficiency, cicadas depend on two different strains of bacteria that they keep cloistered within special cells, and that provide them with additional amino acids. All three partners – the cicadas and the two types of microbes – have evolved in concert, and none could survive on its own.

These organisms together make up what’s known as a holobiont: a combination of a host, plus all of the resident microbes that live in it and on it. The concept has taken off within biology in the past ten years, as we’ve discovered more and more plants and animals that are accompanied by a jostling menagerie of internal and external fellow-travellers. Some of the microorganisms kill each other with toxins, while others leak or release enzymes and nutrients to the benefit of their neighbours. As they compete for space and food, cohabiting microbes have been found to affect the nutrition, development, immune system and behaviour of their hosts. The hosts, for their part, can often manipulate their resident microbiota in many ways, usually via the immune system.

You yourself are swarming with bacteria, archaea, protists and viruses, and might even be carrying larger organisms such as worms and fungi as well. So are you a holobiont, or are you just part of one? Are you a multispecies entity, made up of some human bits and some microbial bits – or are you just the human bits, with an admittedly fuzzy boundary between yourself and your tiny companions? The future direction of medical science could very well hinge on the answer.

The American evolutionary theorist Lynn Margulis, who popularised the theory of symbiosis, first coined the term ‘holobiont’ in 1991. She was interested in long-term, tightly integrated associations such as those evident in lichens – the crusty-looking growths found on rocks and trees, made up of fungus conjoined with algae. Margulis thought that there was a tight analogy between an egg and a sperm coming together to form a new organism, and the coming together of two species to form a new symbiotic consortium, which she called a holobiont.

Margulis argued that the interactions within a holobiont aren’t too different from the life cycle of sexually reproducing organisms. The partners are integrated wholes that die and reproduce as one. But instead of sending out tiny cells to reproduce, holobionts send out individual organisms of different species.

With this framing in mind, when biologists began to use the term in the 1990s, they applied it to a few (usually two) organisms. But the word took on a very different cast in the hands of the American coral reef biologist Forest Rohwer and his colleagues, who defined a holobiont as a host and all of its associated microorganisms.

Two protagonists just aren’t enough when it comes to explaining the evolutionary success of corals. They are made up of clusters of polyps, tiny wiggling things that get by with just a few tentacles and a toothless maw. Coral polyps reproduce by cloning themselves, and then sticking together to form large colonies, supported by a jointly fashioned skeleton. The most spectacular corals work hand-in-hand with photosynthetic algae that they host within their own cells. The algae provide nutrients via photosynthesis, while the coral gives the algae both food and protection. And those simple little polyps don’t end their symbiotic relationships there. Corals don’t possess a complicated immune system to fend off pathogens; instead, they seem to selectively cultivate helpful or benign bacteria, which crowd out the harmful microbes. Corals also produce mucus that appears to be able to trap phages, viruses that infect and kill only bacteria. An enemy of an enemy is a friend, after all.

Rohwer and colleagues, unaware of Margulis’s idea, introduced the term holobiont to capture the dynamics of coral physiology. As a result, by the early 2000s, the scientific literature contained two contrasting definitions. One picked out an organism-like symbiotic pair that reproduced, while the other identified an ecological community of microbes indexed to a host.

For a time, the ecological account prevailed. But Margulis’s physiological conception of holobionts was revitalised in the late 2000s as part of a new theory: what’s known as the hologenome theory of evolution. Advocates merged both versions of holobiont into something a bit more conceptually loaded. On this view, the ecological notion of holobiont (the host and all its resident microbes) is given additional properties. It’s an entity that’s coherent enough to have its own hologenome, made up of the host genome plus all the microbial genomes. A major implication of this theory is that natural selection doesn’t just act on the genome of individual organisms: it acts on the hologenome of holobionts, which are seen as single units that can evolve at the level of the holobiont.

Today, researchers engage in fierce debate over which forces shape holobionts and host-microbiome systems. They can be roughly split into two factions, the ecological and the evolutionary. On the ecological side, holobionts are seen as complex and dynamic ecosystems, in constant flux shaped by individual interactions from the bottom up. So you are part of a holobiont. But this stands in opposition to the evolutionary account, which casts holobionts as higher-level entities akin to organisms or units of selection, and believes that they are shaped as a whole from the top down. On this view, you are a holobiont.

The ecological and evolutionary views make for very different predictions about how a holobiont will change over time. Evolutionary theory predicts that the parts of a unit of selection will tend to cooperate: to sacrifice their own interests for the good of the whole. Ecological theory, by contrast, predicts competition and exploitation: parts will cooperate only insofar as it benefits them. Think of the differences between an ant colony and a motley assortment of insects fighting over scarce resources.

A dominant view in medicine treats the body as a battleground where any invaders are bad and must be exterminated. But in an ecosystem, there are no bad guys, just species playing different roles. If the ecological account of holobionts is true, a human host is more like a habitat to be managed, with the right balance and competition between different kinds of microbes being an important consideration. What counts as healthy can depend on what kinds of services we want out of our attendant ecosystem. If the microbes in a holobiont are more like ants in a colony, or genes in a genome, they are parts of a larger integrated whole. So we might expect stable co-adapted partners living in concert across holobiont generations.

However, the evolutionary version of holobionts gives us reason to stick to an expanded version of the ‘us versus them’ picture of medicine. It’s just that now we have a few more allies on our side that we need to take care of. The evolutionary framework might also provide some justification for the calls for a return to a palaeomicrobiome that existed before the modern diet – for that would literally help to return a missing part of ourselves.

As things stand, the evidence leans heavily towards a more ecological interpretation of holobionts. Most of the partners come together anew each generation, and don’t interact in the ways that are necessary for higher-level integration into organismic wholes. The theoretical bar for making that transition is high, and getting over it is going to be rare. But it potentially varies from holobiont to holobiont. There is still a long and exciting scientific road ahead, as researchers begin to unravel the secret lives and complex effects of microbes on the development, behaviour and evolution of their hosts.

Derek J. Skillings is a biologist and philosopher of science and currently a lecturer in philosophy at the University of Pennsylvania.

This article was originally published at Aeon and has been republished under Creative Commons.

New Timescale: Ancestor of All Life on Earth Evolved Earlier Than We Thought

A recent study, approaching the construction of a timescale for life in a new way, indicates that life on Earth may have begun before originally expected.

Science may have enabled us to travel in space and trace the history of the entire universe, but it has not yet been able to answer exactly how and when life first arose on our planet. Traditionally, scientists have used the fossil record to try to answer these questions. Yet, as palaeontologists are all too aware, fossils are increasingly hard to find as we move backwards in time.

In fact, we don’t have a lot of rock available to study that is older than two-and-a-half billion years. This is due to the Earth’s rock recycling system in which old rocks are destroyed through weathering processes, with the remains getting recycled into new rocks. This causes any rocks that we do have to be highly reworked from their original composition. Often they don’t contain any biological remains at all. Even the rare fossils that we do find are often very difficult to identify and cannot be easily linked to any specific group of modern organisms.

In our new study, published in Nature Ecology and Evolution, we decided to try and approach the construction of a timescale for life in a new way. This involved using the wealth of genetic data that we now have for organisms living today and applying a molecular clock, a method to decipher the past by reading the stories written in the genes of living organisms.

All life inherits genetic information from the previous generation, and this gradually changes over time as evolutionary events take place. The methodology works on the basis that the differences in the genomes of two extant (living) species, for example a human and a bacterium, have accumulated in a manner that is roughly proportional to the time since they had a common ancestor. Fossils still play a vital role in this approach by acting as a rough guide to the age of common ancestors, and the molecular clock is used to update these estimates.

Our study combines the molecular data of 29 genes from a total of 102 living organisms (we also used nine fossils for calibration). The living organisms come from right across the tree of life – including bacteria, archaea (single-celled microorganisms) and eukaryotes (multi-celled organisms such as plants and animals).

Including fossils in the process is vital to the analysis because they help to link the events in real time. Fossils tell us that a lineage must have existed prior to the age of the fossil, simply because the fossil is there. This method is most important for the reconstruction of life at its earliest points, because we have so little fossil material to work with. However, until now, this is precisely where it has been applied the least.

A timescale for the evolution of life on Earth summarising the findings of the new study. Credit: University of Bristol

Our results – a timescale for the origin and evolution of life – do come with fairly large uncertainties on the age estimates for each of the nodes, the places on the tree where species have a common ancestor. This is especially true for the most ancient parts of the tree and those parts where we have the least data, either fossil or molecular.

However, the fact that we capture uncertainty is promising, as it indicates that our timescale is not over confident by showing precise, but false, ages. Instead it means that as new extant lineages and fossils continue to be discovered, they can be added to the analysis to both refine and update it – possibly resulting in a higher degree of precision in the future.

The ancestor of all organisms

We find that the “last universal common ancestor” – a hypothetical very early single cell from which all life on Earth descended – existed prior to the “late heavy bombardment”. This was a period of intense meteor bombardment sustained by our planet about 3.9 billion years ago. This is significantly earlier than the currently accepted oldest fossil evidence would suggest (estimating 3.5-3.8 billion years ago).

The oldest confirmed fossils are from about 3.4 billion years ago, while the oldest potential fossils have been found on Greenland and date back to about 3.8 billion years ago. There’s also a suggestion that carbon found in a 4.1 billion-year-old mineral called zircon could be biological in nature. However, scientists have so far been unable to confirm that.

Some researchers think it would have been impossible for life to survive the late heavy bombardment, so that our oldest ancestor must be from after this phase. There are claims that the event would have sterilised the plants and vaporised any water around at the time. However, there are some recent mathematical models which suggest that pockets suitable for life could have remained.

We found that the crown groups of the two main lineages of life – bacteria and archaea – appeared almost one billion years after the last common universal ancestor. Eukaryotes, on the other hand, diverged relatively late in Earth’s history, about 1.8 billion years ago. This finding is consistent with previous studies.

Our timescale also allowed us to look at ancient events such as the “mitochondrial endosymbiosis” – the process which formed the mitochondria, the organelles that power our cellular respiratory systems. This important event in the history of the eukaryotes occurred close to when they first appeared, suggesting that it helped to drive their subsequent rapid spread.

We hope that our study will be a good starting point for probing the mysteries of evolution at this extremely early time in Earth’s history.

Holly Betts, PhD candidate in Paleobiology, University of Bristol.

This article was originally published on The Conversation. Read the original article.

How a Battleground Between Bacteria and Viruses Is Being Used for Human Health

Viruses can’t replicate on their own, so they infect other organisms and hijack their cellular machinery to produce viral offspring. To defend themselves, bacteria evolved CRISPR/Cas.

Evolution is both fascinating and horrifying in its ruthlessness. The strong survive and proliferate, while the weak are mercilessly done away with. All around us, billions of microorganisms such as fungi, bacteria, and viruses are constantly at war in environments that have limited nutrients. In fact, understanding these war tactics enabled the discovery of penicillin, a chemical compound produced by a fungus called Penicillium chrysogenum. This compound inhibits the growth of pathogenic bacteria, such as Staphylococcus, by weakening the structure of their cell walls, eventually causing cell death by explosion. Viruses are no less vicious; since they cannot replicate on their own, they infect other organisms, hijack their cellular machinery to produce viral offspring, and kill their hosts. To defend themselves against viral infections, bacteria evolved the CRISPR/Cas system.

CRISPR stands for clustered regularly interspaced short palindromic repeats, a mouthful for an elegant mechanism of self-defence. Consider the following situation: Team A and Team B are locked in a perpetual battle. Team A is always trying to invade Team B’s territory and capture all its resources. Every member of Team A carries identical ID cards and when one member of Team A invades Team B’s territory, Team B captures the ID card and stores a copy in its database. The next time another member of Team A tries the same thing, Team B compares the two ID cards. If it’s a perfect match, the invading Team A member is destroyed. This is essentially what happens between bacteria (Team B) and phages (Team A), the viruses that infect bacteria.

Figure 1: How CRISPR/Cas immunity works. Credit: Club SwiWri

Bacteria (Team B) make use of the fact that a phage (Team A) injects its genetic material during an infection. The bacteria cut the material in specific locations to create protospacers. These protospacers are then copied and modified to produce spacers, which are integrated into the bacterial genome within the CRISPR locus. Therefore, the bacteria are able to permanently maintain a record of the information carried in the spacer sequence. CRISPR refers to the short, repetitive sequences that separate each unique spacer sequence. As shown in the figure, Spacer 1, Spacer 2, and Spacer 3 can come from several different phages, therefore each bacteria has a unique sequence stored in its genetic database. Upon subsequent infection, the bacteria utilise the Cas proteins, such as Cas9, to compare the spacer sequences they acquired from the previous infection to the sequence of the invading phage. If the copies match, the bacteria proceed to destroy the invading genetic material by cutting it up completely.

There are several diverse uses of CRISPR sequences- since they are unique, the spacers can be used to identify the bacteria that carry them. For example, although the current methods of detecting Salmonella infections are extremely accurate, they are technically demanding; hence, difficult to implement in poorer countries. Additionally, these methods are non-automated, which delays detection. However, identification of ‘signature’ CRISPR sequences can be automated, thus helping detect bacterial pathogens and thereby the corresponding bacterial subtype, quickly and accurately. CRISPR sequences have also found a place in the dairy industry – for cheese production. The cheese-making process requires very high densities of bacterial cultures, thus making them extremely vulnerable to phage infections, which can kill the entire bacterial population. The introduction of CRISPR sequences into these bacteria makes them resistant to phage infections thereby eliminating production problems.

The most exciting applications of the CRISPR/Cas9 technology, however, are based on the fact that Cas9 proteins can create precise double-stranded DNA breaks. Therefore, these proteins can be guided to precisely edit host DNA sequences resulting in insertion, deletion, or other changes in the genetic sequence. Furthermore, since the technology is simple, it can be used to modify several targets simultaneously, and can be used in a wide range of eukaryotic organisms, ranging from yeast to humans. A further improvement on this system is the use of a protein called Cpf1, instead of Cas9, which enables new targeting possibilities and improves the efficiency of genetic insertions.

Figure 2: Types of DNA manipulation that can be accomplished with the CRISPR/Cas9 system. Credit: Club SciWri

The DNA of interest is cut using Cas9. The eukaryotic cell can then process the DNA via either of two distinct pathways: Pathway 1 that joins cut ends, which can either result in a loss of genetic information (deletion) or insertion of a new sequence between the cut ends or Pathway 2 where the missing DNA sequence is rebuilt by using the other copy of host DNA which contains the intact sequence as a template.

Where can we use this gene manipulating ability of the CRISPR/Cas9 system? One of the most exciting applications is to kill bacterial pathogens. Antibiotic resistance is becoming one of the most pressing health problems in the world today. One potential way to deal with these drug-resistant bacteria would be to make specific deletions in their sequence, say by targeting essential genes, using CRISPR/Cas9. To do so, a cocktail of phage that contain the CRISPR message would be introduced into the body, the phage would then target the pathogenic bacteria, therefore leading to their destruction. Of course the irony is that the CRISPR system, which bacteria use to kill phage, would now being harnessed to make phage kill bacteria. The added advantage of this system would be that the natural, non-pathogenic bacteria in the body would remain untouched, which is not the case when antibiotics are used.

So why is there controversy surrounding the CRISPR/Cas9 system? As discussed before, CRISPR/Cas9 can make very specific genetic modifications. This trait can be immensely useful when the technique is used to cure diseases such as cataract disorders, Duchenne muscular dystrophy and treat viral infections such as HIV and hepatitis B. However, this ability to manipulate genes may lead to potentially unethical practices, such as eugenic selection of traits in human embryos.

This genetic modification process may also have off-target effects, where changing one gene may lead to unintended changes in other genes. Although there is no convincing data that indicate such undesired effects, they still remain a concern. With these issues in mind, in 2015, the members of the national scientific communities of America, Britain and China agreed that the technology would only be used for basic research provided that the legal and ethical guidelines were followed. Further, the technology would be utilised only for somatic cells, where only a single individual would be affected, rather than for germ cells, where gene modifications would be inherited by the offspring and could therefore affect human evolution.

A more concerning problem was recently published, where researchers found that CRISPR could lead to large-scale DNA deletions and rearrangements. Granted that this unwanted side effect is not unique to CRISPR and can happen with other gene-editing tools, the finding calls for increased vigilance among researchers. Usually CRISPR is used to create small deletions to knock out the effect of a gene. However, close investigation seems to suggest that larger deletions are present in the vicinity of the target gene. Although these side effects are concerning, careful experimental design and sequencing of the target DNA including the surrounding sequences should go a long way in avoiding this danger. Nevertheless, the applications of CRISPR/Cas9 are exciting and can have far-reaching medical uses, which can make (many) life-threatening genetic conditions a thing of the past.

This article was originally published on Club SciWri and has been republished here with written permission.

Most People Don’t Benefit From Vaccination, But We Still Need It To Prevent Infections

Stating that a majority of people won’t benefit from a vaccine ignores the purpose of immunisation programmes.

A recent article in The Conversation questioned whether we should all get flu vaccinations, given 99 people would have to go through vaccination for one case of flu to be prevented.

But this position ignores the purpose of immunisation programs: whole populations of people need to take part for just a small number to benefit. So how do we decide what’s worth it and what’s not?

Decision-making in public health

When we consider a treatment for a patient, such as antibiotics for an infection, we first consider the evidence on the benefits and potential harms of treatment. Ideally, this is based on clinical trials, where we assume the proportion of people in the trial who respond represents the chance an individual patient will respond to treatment.

This evidence is then weighed up with the individual patient. What are the treatment options? What do they prefer? Are there factors that might make this patient more likely to respond or have side effects? Is there a treatment alternative they would be more likely to take?

In public health, the framework is the same but the “patient” is different – we are delivering an intervention for a whole population or group rather than a single individual.

We first consider the efficacy of the intervention as demonstrated in clinical trials or other types of studies. We then look at which groups in the population might benefit the most (such as the zoster vaccine, given routinely to adults over 70 years as this group has a high rate of shingles), and for whom the harms will be the least (such as the rotavirus vaccine, which is given before the age of six months to reduce the risk of intussusception, a serious bowel complication).

Compared to many other public health programmes, immunisation is a targeted intervention and clinical trials tell us they work. But programs still need to target broad groups, defined by age or other broad risk factors, such as chronic medical conditions or pregnancy.

Risks and benefits of interventions

When considering vaccination programs, safety is very important, as a vaccine is being given to a generally healthy population to prevent a disease that may be uncommon, even if serious.

For example, the lifetime risk of cervical cancer is one in 166 women, meaning one woman in 166 is diagnosed with this cancer. So even if the human papillomavirus (HPV) vaccine was completely effective at preventing cancer, 165 of 166 women vaccinated would not benefit. Clearly, if we could work out who that one woman was who would get cancer, we could just vaccinate her, but unfortunately we can’t.

It’s only acceptable to vaccinate large groups if clinically important side effects are low. For the HPV vaccine, anaphylaxis (a serious allergic reaction) has been reported, but occurs at a rate of approximately one in 380,000 doses.

An even more extreme case is meningococcal vaccination. Before vaccination, the incidence of meningococcal serogroup C (a particular type of this bacterium) infection in children aged one to four years old was around 2.5 per 100,000 children, or 7.5 cases for 100,000 children over three years.

Vaccination has almost eliminated infection with this strain (although other serotypes still cause meningococcal disease). But this means 13,332 of 13,333 children didn’t benefit from vaccination. Again, this is only acceptable if the rate of important side effects is low. Studies in the US have not found any significant side effects following routine use of meningococcal vaccines.

This is not to say there are no side effects from vaccines, but that the potential side effects of vaccines need to be weighed up against the benefit.

For example, Guillain Barre syndrome is a serious neurological complication of influenza vaccination as well as a number of different infections.

But studies have estimated the risk of this complication as being around one per million vaccination doses, which is much smaller than the risk of Guillain Barre syndrome following influenza infection (roughly one in 60,000 infections). And that’s before taking into account the benefit of preventing other complications of influenza.

What other factors need to be considered?

We also need to consider access, uptake and how a health intervention will be delivered, whether through general practices, council programs, pharmacies or school-based programmes.

Equity issues must also be kept in mind: will this close the gap in Indigenous health or other disadvantaged populations? Will immunisation benefit more than the individual? What is the likely future incidence (the “epidemic curve”) of the infection in the absence of vaccination?

A current example is meningococcal W disease, which is a new strain of this bacteria in Australia. Although this currently affects individuals in all age groups, many state governments have implemented vaccination programs in adolescents.

This is because young adults in their late teens and early 20s carry the bacteria more than any other group, so vaccinating them will reduce transmission of this strain more generally.

But it’s difficult to get large cohorts of this age group together to deliver the vaccine. It’s much easier if the program targets slightly younger children who are still at school (who, of course, will soon enter the higher risk age group).

In rolling out this vaccine program, even factors such as the size of schools (it is easier to vaccinate children at high schools rather than primary schools, as they are larger), the timing of exams, holidays and religious considerations (such as Ramadan) are also taken into account.

For government, cost effectiveness is an important consideration when making decisions on the use of taxpayer dollars. This has been an issue when considering meningococcal B vaccine. As this is a relatively expensive vaccine, the Pharmaceutical Benefits Advisory Committee has found this not to be cost effective.

This is not to say that meningococcal B disease isn’t serious, or that the vaccine isn’t effective. It’s simply that the cost of the vaccine is so high, it’s felt there are better uses for the funding that could save lives elsewhere.

While this might seem to be a rather hard-headed decision, this approach frees up funding for other interventions such as expensive cancer treatments, primary care programs or other public health interventions.

Why is this important?

When we treat a disease, we expect most people will benefit from the treatment. As an example, without antibiotics, the death rate of pneumonia was more than 80%; with antibiotics, less than 20%.

However, vaccination programmes aim to prevent disease in whole populations. So even if it seems as though many people are having to take part to prevent disease in a small proportion, this small proportion may represent hundreds or thousands of cases of disease in the community.

Allen Cheng, Professor in Infectious Diseases Epidemiology, Monash University

This article was originally published on The Conversation. Read the original article.

Have Scientists Discovered the Germ Responsible for Killing 15 Million Aztecs?

Despite new findings, the deaths can’t be blamed on enteric fever alone.

Aztec sculpture. Credit: Wikimedia Commons

This week, dozens of media outlets declared that scientists had solved the mystery of what wiped out the Aztecs. Traces of a pathogen that can cause a typhoid-like enteric fever have been found in skeletons from a cemetery linked to the catastrophic epidemics of 1545-50, which killed millions of indigenous people in 16th century Mexico.

One of three pandemics that brought about the collapse of native populations in Central America, the 1545 outbreak was caused by an unknown disease, which is described in the sources as “cocoliztli”. The new study, published in Nature, Ecology & Evolution, speculates that the origin was a rare strain of salmonella called paratyphi C. But from my point of view, as an indigenous historian, this claim is problematic.

Cocoliztli, a Nahuatl (Aztec language) term, is usually translated as “pestilence”, but the word actually suggests “pustules” or breaking through the skin, issues not usually connected to enteric fever. Indigenous sources like the Codex en Cruz (a pictorial codex) show spots and nose bleeds as the main symptoms, and extreme bleeding is also mentioned regularly in Spanish accounts.

This matches recent scholarly opinion, which has tended to favour an unknown form of haemorrhagic fever, similar to Ebola, as the cause of cocoliztli. But it is possible that spots and nosebleeds were simply the easiest symptoms to draw, as well as being the most obvious markers of disease to people probably suffering from multiple unknown illnesses. We are not even sure that the term cocoliztli had a consistent meaning. It first pops up in reference to what was almost certainly a smallpox epidemic in 1519-20.

Worst death tolls in history

The death of millions of indigenous Americans after the European invasion is one of the great tragedies of the modern era. Even using the most optimistic estimates, at least 80% of the pre-contact population of Mexico died in the first century after the Spanish arrival.

With one of the worst death tolls in history – more than 90% in some areas – the devastation is almost incomprehensible. Try to imagine nine out of every 10 people you know dying in the next decade: the devastation of families, the loss of children, the decimation of communities, being unable to care for dying relatives because you are so sick yourself.

There is a natural desire to find a single cause for events, to try and make a tragedy explicable, to understand what “really” happened. But such appalling mortality rates were not caused by a single, devastating plague. They reflect people who, lacking immunity to European diseases and suffering under colonialism, were battered by wave after wave of germs – including flu, typhus, measles, smallpox and, almost certainly, enteric fever.

Major epidemics tended to follow times of famine and drought and were worsened by colonial policies that herded indigenous people into more easily manageable settlements. Already exhausted and living in close quarters, with little idea how to cope with these new illnesses, indigenous people died in huge numbers.

The Nature study itself is admirably measured, resisting the temptation (unlike headline writers) to declare enteric fever as the cause of the cocoliztli outbreak. And the new DNA analysis tool used in the study, which offers for the first time a way of scanning for all known bacterial pathogens, opens exciting new possibilities for research into historical DNA.

But it doesn’t tell us – as the authors themselves freely admit – whether salmonella was responsible for the 1545 epidemic. It is not even certain (although it is highly likely) that the people studied suffered from enteric fever. We know only that they were exposed to the bacteria. This is an important finding, and the research method opens the way for future studies that may shed further light on this historical catastrophe.

Unfortunately, this research can’t definitively tell us what killed the Aztecs in this dreadful way, and science can only ever tell part of the story. As the Franciscan friar Bernardino de Sahagún recorded:

People with the illness could not walk…they could not move; they could not stir. And when they stirred, they screamed. The pustules that covered people caused great desolation; a great many people died of them, and many just died of hunger; [for] no one took care of others any longer.

To disentangle a single disease from the bacterial and viral soup that existed in 16th-century Mexico is not only impossible, it obscures the reality of cocoliztli.

Caroline Dodds Pennock is a lecturer in international history at the University of Sheffield.

This article was originally published on The Conversation. Read the original article.

How Bacteria Defend Themselves Against Lethal Antibiotics

In a new IISc-IISER study, researchers have shown how bacteria take the help of hydrogen sulphide gas to defend themselves.

Scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells. Credit: Rocky Mountain Laboratories, NIAID, via wikimedia commons

Scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells. Credit: Wikimedia Commons

In a new study, researchers from Indian Institute of Science (IISC), Bangalore and Indian Institute of Science Education and Research (IISER), Pune have shown how bacteria take the help of hydrogen sulphide (H₂S) gas to defend themselves against the onslaught of antibiotics. The study was published in Chemical Science.

Antibiotics usually kill bacteria by inducing oxidative stress leading to accumulation of reactive oxygen species (ROS), that damage bacteria’s essential machinery – DNA and enzymes. Interestingly, when antibiotic-resistant bacteria encounter such oxygen-rich environments, they produce H₂S that scavenges the excess ROS and protects the cell from damage.

To be able to study how H₂S affects resistant bacterial cells, the team devised an innovative system for generating H₂S inside living bacterial cells. They designed a new compound, cyclopentane-1,1-diylbis((4-nitrobenzyl) sulfane, “which is a substrate for E. coli’s nitroreductase enzyme (NTR) and releases H₂S in presence of the enzyme inside the cell,” explains Prashant Shukla, PhD student at IISc, Bangalore, and one of the authors of this study.

The NTR enzyme is expressed exclusively in bacteria and not in mammalian cells. “We wanted to exclude possibilities of host-derived H₂S playing a role in our experiments with intracellular pathogens such as Salmonella and Mycobacterium.” says Harinath Chakrapani, associate professor at IISER, Pune and an author on the paper.

The designed donor was able to permeate inside healthy bacterial cells while retaining their functionality. When donor loaded bacterial cells were exposed to hydrogen peroxide (H₂O₂), which is a good source of ROS, the H₂S released by donor present inside the bacterial cells was able to reduce it and protect the cell from damage.

The authors also examined whether elevated endogenous H₂S levels showed a positive correlation with drug resistance in human infections. “We measured the intracellular H₂S levels of several multidrug-resistant (MDR) E. coli strains isolated from patients suffering from urinary tract infections (UTI). The endogenous H₂S levels were considerably higher than non-pathogenic strains (of bacteria) indicating a possible functional role for H₂S in antibiotic resistance,” says Shukla. The authors were also able to show that inhibition of H₂S biosynthesis reversed antibiotic resistance in MDR varieties of UTI-causing bacteria. UTI affects millions in India and indiscriminate use of antibiotics has made UTI pathogens resistant to most antibiotics.

Amit Singh, assistant professor at IISc and one of the authors of the study, says, “A combination of molecules/drugs targeting H₂S biosynthesis, antioxidants, and an alternate route of respiration could have a remarkable impact on reversing drug resistance and clinical outcomes”.

Vasanthi Ramachandran, director of the microbiology division at Bug Works, who is unrelated to the study, says, “The authors have used a novel approach to substantiate the role of H₂S towards antibiotic resistance.”

“The study has definitely shown and opened up newer avenues including novel targets that can be exploited to understand and overcome resistance,” she added.

This article was originally published by IndiaBioscience.

NASA Scientists Name Bacterium Found on ISS After Abdul Kalam

Even though Solibacillus kalamii has not yet been found on Earth, it is really not an extraterrestrial lifeform, either.

A view of the International Space Station. Credit: tpsdave/pixabay

Los Angeles: A team of scientists at NASA has named a new organism discovered by them after A.P.J. Abdul Kalam, a former president of India. Till date, the new lifeform – a bacterium – has been found only on the International Space Station (ISS) and has not been found on Earth.

Researchers at NASA’s Jet Propulsion Laboratory (JPL), California, which works on interplanetary travel, discovered the new bacterium on filters installed on the ISS. They have named it Solibacillus kalamii to honour the late president, who was an aerospace scientist. Kalam had his early training at NASA in 1963 before he set up India’s first rocket-launching facility in the fishing village of Thumba in Kerala.

“The name of the bacterium is Solibacillus kalamii, the species name is after Abdul Kalam and genus name is Solibacillus, which is a spore forming bacteria,” said Kasthuri Venkateswaran, a senior research scientist at the Biotechnology and Planetary Protection Group at JPL.

The filter on which the new bug was found remained on board the ISS for 40 months. Called a high-efficiency particulate arrestance (HEPA) filter, it is a component of the routine housekeeping and cleaning system. This filter was later analysed at JPL. Venkateswaran published his discovery in the International Journal of Systematic and Evolutionary Microbiology this year. According to him, even as it orbits Earth at some 400 kilometres altitude, the ISS is home to many types of bacteria and fungi that cohabit the station with the astronauts who live and work there. He added that even though S. kalamii has not yet been found on Earth, it is really not an extraterrestrial lifeform, either.

“I am reasonably sure it has hitch hiked to the space station on board some cargo and then survived the hostile conditions of space,” explained Venkateswaran.

Naming the new microbe after Kalam was natural to Venkateswaran and his team. “Being a fellow Tamilian, I am aware of the huge contributions by Kalam,” he said. New bacteria are usually named after famous scientists. Venkateswaran is a part of a team exploring the possibilities of alien life, and towards that his responsibilities include monitoring bug-levels on the ISS. He also has to ensure all spacecraft that fly to other planets are free of terrestrial bugs. For example, one of his tasks had been to ensure that NASA’s Curiosity, the car-sized almost-1,000-kg rover, was totally sterile when it left Earth for Mars.

According to international law, these exacting hygiene levels are required because, otherwise, other planets could get contaminated by living things from Earth.

Today, the ISS is the size of a football field and has the distinction of being the largest human-made object to be orbiting Earth. Its construction started with a launch in 1998. It weighs about 419 tonnes, can house a maximum of six astronauts at a time and has cost roughly $150 billion to build and maintain. To this day, 227 astronauts have flown to the space station. As a result, keeping it clean is critical, so that humans can live on it with relative ease. All air and water is is recycled because it is a completely closed environment. Any mould or fungi has to be removed immediately while all the walls have to be constantly protected from corrosion.

Venkateswaran’s main job is to monitor the environment of the station so that harmful bugs do not proliferate. He heads the microbial observatory on the ISS, which studies microorganisms associated with compartments owned by the US. According to NASA, he also directs several research and development tasks for JPL’s Mars Program Office, which oversees the cleaning, sterilisation and validation of spacecraft components.

(PTI)

Canadian Bacteria-Like Fossils May Be Oldest Evidence of Life Yet

It was primordial microbes, like those described in a recent study, that set in motion the evolutionary march toward complex life and, eventually, the appearance of humans 200,000 years ago.

World’s oldest fossil discovered in Canada. Credit: Wikimedia Commons

Washington: Microfossils up to almost 4.3 billion years old found in Canada of microbes are similar to the bacteria that thrive today around sea floor hydrothermal vents and may represent the oldest-known evidence of life on Earth, scientists said on Wednesday (March 1).

The fossils from the Hudson Bay shoreline in northern Quebec near the Nastapoka islands lend credence to the hypothesis that hydrothermal vents spewing hot water may have been the cradle of life on Earth relatively soon after the planet formed, the researchers said.

Haematite tubes from the NSB hydrothermal vent deposits in Quebec, Canada that represent the oldest microfossils and evidence for life on Earth are pictured in this undated handout photo obtained by Reuters March 1, 2017. The remains are at least 3,770 million years old. Credit: Reuters

They also said Earth’s planetary neighbour Mars at that time is thought to have had oceans, long since gone, that may have boasted similar conditions conducive to the advent of life.

Tiny filaments and tubes made of a form of iron oxide, or rust, formed by the microbes were found encased in layers of quartz that experts have determined to be between 3.77 billion and 4.28 billion years old, according to the study published in the journal Nature.

The researchers expressed confidence the fossils from northeastern Canada were formed by organisms, saying no non-biological explanation was plausible.

It was primordial microbes like those described in the study that set in motion the evolutionary march toward complex life and, eventually, the appearance of humans 200,000 years ago.

“Understanding how and when life began on Earth helps answer the long-standing questions: Where do we come from? Is there life elsewhere in the universe?” said study researcher Matthew Dodd, a University College London biogeochemist.

A haematite filament enveloped by a fine irregular layer of nanoscopic haematite from vent deposits in the Nuvvuagittuq Supracrustal Belt in Québec, Canada is pictured in this undated handout photo obtained by Reuters March 1, 2017. These filaments of iron, about half the size of a human hair, were made by primitive microbes involved in the carbon and iron cycles. Credit: Reuters

The scientists said the primordial microbes’ structure closely resembled modern bacteria that dwell near iron-rich hydrothermal vents. They believe that, like their modern counterparts, they were iron-eaters. The rock’s composition was consistent with a deep-sea vent environment.

“This is important for the origin of life,” said study researcher Dominic Papineau, a University College London astrobiologist. “It shows microbial life diversified to specialised microbes very early in Earth history.

“It is also important for the evolution of life. It shows that some microbes have not changed significantly” since Earth’s early times, Papineau said.

Earth formed about 4.5 billion years ago and the oceans appeared about 4.4 billion years ago. If the fossils are indeed 4.28 billion years old, that would suggest “an almost instantaneous emergence of life” after ocean formation, Dodd said.

The fossils appear to be older than any other previously discovered evidence of life. For example, other scientists last year described 3.7 billion-year-old fossilized microbial mats, called stromatolites, from Greenland.

(Reuters)